Prepare

[ckmah]

Improvements to IO and feature computations

• bento.io.prepare(): first stab at ingesting external molecular and segmentation data 1fb026b
  • first assigns secondary seg. masks to cell in a 1-to-1 fashion
  • indexes points to cells and mapped sec. shapes
• bento.tl.analyze_samples: sample computation memory usage is now tractable
  • naive dask partitioning only accounted for memory footprint of points dataframe, but memory blowup comes from MultiIndex groupby operations
  • custom partitioning ensures partitions have capped number of groupby groups
  • in the future make it a user parameter? needs more testing
• some progress bars and emojis :cake:

[codecov-commenter]

Codecov Report

Merging #64 (d6844ac) into master (f9ca5fe) will increase coverage by 1.86%. The diff coverage is 36.72%.

@@            Coverage Diff             @@
##           master      #64      +/-   ##
==========================================
+ Coverage   56.70%   58.57%   +1.86%     
==========================================
  Files          24       24              
  Lines        1379     1359      -20     
==========================================
+ Hits          782      796      +14     
+ Misses        597      563      -34     

Impacted Files	Coverage Δ
bento/_utils.py	75.75% <ø> (ø)
bento/io/__init__.py	100.00% <ø> (ø)
bento/preprocessing/_preprocessing.py	86.66% <ø> (+37.39%)	:arrow_up:
bento/plotting/_plotting.py	15.15% <6.45%> (+1.51%)	:arrow_up:
bento/io/_io.py	16.87% <14.73%> (-0.96%)	:arrow_down:
bento/tools/_cell_features.py	55.00% <66.66%> (+3.40%)	:arrow_up:
bento/preprocessing/__init__.py	100.00% <100.00%> (ø)
bento/tools/_lp.py	41.22% <100.00%> (ø)
bento/tools/_sample_features.py	98.08% <100.00%> (+2.04%)	:arrow_up:
tests/test_sample_features.py	100.00% <100.00%> (ø)
... and 3 more

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